Style lets you change the style of the selected region of the molecule eg to spacefill or cartoon view.Ītoms lets you hide atoms or change their size in the selected region of the molecule. Reset lets you reset the position of the structure, reset the appearance of the structure to the default, or reset the appearance of the structure to its appearance when it was last saved.Ĭolor lets you change the color scheme of the selected region of the atom. Here you can modify the appearance of the structure. Īt the top of the viewer is the display menu. For a complete description of the commands you can use, see. To see some examples, select one of the pre-populated options in the box's drop-down. The command box lets you type in arbitrary jmol scripting commands. You can also Shift-click and Ctrl-click to select multiple regions at once. Click on regions in the tree to select those regions. The structure tree shows the atoms in the structure in a tree format. The highlight selected checkbox lets you select whether to highlight the selected atoms in the structure view. The select button lets you select all, none or the nonselected region of the structure, as well as by element, group type or secondary structure. If the structure you are viewing contains more than one model, the model combo box will you choose between them. To the right of the structure are controls that let you control the selected part of the structure. Hold the Ctrl key then right-click and drag to pan, or, if you are using a Mac, click and hold, press Ctrl and Alt/Option then drag to pan. Hold the Alt or Shift key then click and drag to zoom in/out 3D protein structure viewerįor molecular structure documents, such as PDB documents, this displays an interactive three dimensional view of the structure.Ĭlick and drag the mouse to rotate the structure. Color by probability is only available when using the Partition Function.Ĭompute Options will rerun RNAfold when you change their settings, so depending on the size of the sequence there may be a noticeable recompute time. Green is the middle ground and blue is the lowest probability. In addition, when in split view mode, the fold viewer will scroll to the selected area when zoomed in.īy default, Color by probability is used where red bases are the ones with the strongest probability of the bases being paired with each other in paired regions, or being unpaired in unpaired regions. Selection is synchronized between the sequence view and the fold view. As with other viewers, you can zoom in on the model and drag the view around, or use the scrollwheel using the same keyboard modifiers as the sequence viewer. The View Options allow you to turn off/on and color the bases, flip the coordinates, highlight the start (blue) and end (red) of the sequence and rotate the model. Information on the options for this tool can be found at the following web page. The fold prediction is performed by the Vienna package RNAfold tool. If the selected sequence is DNA, the tab will be labelled DNA Fold and if it is RNA it will be labelled RNA Fold. This will show the tab for any sequence less than 3000 bp. If you wish to use RNA fold on a non-oligo sequence, go to Tools → Preferences → Appearance and Behavior and enable the option Show DNA/RNA fold view on all sequence. This study provides a reference for the dynamic changes of the gut virome after human Enterovirus infection, which may help guide the rational drug use in clinical treatment and provide new ideas for preventing Enterovirus infection.RNA, DNA and Protein Structure Viewer RNA/DNA secondary structure fold viewerīy default this viewer is only shown when an oligo sequence is selected. We proposed that Caudovirales and Microviridae may be biomarkers for the Coxsackievirus infection process. The gut virome had significant variations with the increase of Caudovirales and the decrease of Microviridae after infection. We found that the mice virome was dominated by Caudovirales and Microviridae, and phylogenetic analyses showed that both Caudovirales and Microviridae had high diversity. Here, we established the mouse model of Coxsackievirus B3 infection and collected fecal samples at several time points to investigate alterations of the gut virome using viral metagenomic analysis.
Coxsackievirus B3 infects millions of humans yearly and yet limited research has explored dynamic alterations of the gut virome after infection.
The gut microbiome plays an essential role in the human health and dysbiosis has been implicated in numerous diseases.
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